Premières données de l’étude par radio-pistage VHF des déplacements des chats dans un site majeur de reproduction du Puffin Yelkouan, endémique de Méditerranée

Le chat représente un des prédateurs invasifs les plus menaçants pour les espèces natives des îles et particulièrement pour les oiseaux marins adultes qui sont fortement vulnérables à la prédation. Les populations du Puffin Yelkouan, espèce endémique du bassin méditerranéen, sont réparties en quelques grandes colonies de reproduction et sont en voie de déclin, notamment du fait de l’impact des chats harets et errants. Dans une étude précédemment publiée, l’impact des chats introduits sur la population de puffins de l’île du Levant a été évalué au travers du régime alimentaire du chat sur une période de deux ans. Cette étude a mis en évidence que les chats consommaient trois proies principales : le Lapin, le Rat noir et le Puffin Yelkouan, et qu’un pic de prédation de puffins était observé dès leur arrivée sur les colonies (période de prospection). Nous avons donc cherché à compléter ce travail par une étude préliminaire visant à étudier les patrons de mouvement de quatre chats (trois chats harets et un chat domestique) via un suivi VHF (very high frequency), dans le but d’analyser leurs comportements individuels et leurs domaines vitaux sur l’île du Levant, qui est l’un des principaux sites de reproduction du Puffin Yelkouan. Nos résultats montrent que deux des trois chats harets ont été détectés dans les colonies de puffins durant les périodes de prospection et de reproduction de cet oiseau marin alors que le chat domestique n’a jamais été détecté dans ces colonies. Cela suggère que les patrons de déplacement des quatre chats suivis puissent être liés à la présence des puffins dès que ces oiseaux marins arrivent à la colonie. Les chats suivis montrent des domaines vitaux de taille relativement réduite, plus larges pour les chats harets qui couvrent de plus grandes distances, et avec des territoires chevauchants, que pour le chat domestique. Ces résultats préliminaires de patrons de déplacements, couplés aux résultats précédents de prédation du chat sur le Puffin Yelkouan, nous indiquent que l’impact du chat haret se doit d’être limité. Cet objectif doit être atteint en effectuant une stratégie de gestion efficace qui tiendrait compte des patrons de déplacements des chats afin d’éviter l’épuisement d’un des sites de reproduction les plus importants pour cette espèce de puffin endémique de MéditerranéeCats are considered one of the most harmful invasive predators of island native species, particularly adult shearwaters, which are highly vulnerable to predation. Populations of Yelkouan shearwater, an endemic species of the Mediterranean basin with only a few large breeding colonies, are predicted to decline in response to feral or free-roaming cats. In a previous study, the impact of introduced cats on the Yelkouan shearwater population of Le Levant Island was assessed through the analysis of cat diet over a two-year period. The study showed that cats prey upon three staple species: rabbits, rats, and shearwaters, with a peak of predation on shearwaters immediately upon their arrival at colonies (prospecting period). Here, we supplement this previous work by conducting a preliminary study on the movement patterns of four free-roaming cats (three feral and one domestic) using very high frequency (VHF) tracking to analyse individual behaviour and home ranges on Le Levant Island, one of the Yelkouan shearwater’s major breeding sites. Our results show that two of the three feral cats were recorded inside and in close vicinity to the shearwater colonies, mainly during the prospecting period, while the domestic cat was never recorded inside the colonies. This suggests that some feral cats could show movement behavioural patterns linked to the shearwater presence as soon as these seabirds arrive at the colonies. The monitored domestic cat also showed a relatively small home range, while feral cats covered larger distances and with overlapping territories. Based on these preliminary results of cat movement behaviour, in addition to the previous results of cat predation, it is evident that cat impact must be reduced. This may be achieved through accurate management strategy that takes cat movement behaviour into account to avoid exhausting one of the most important breeding sites for this Mediterranean endemic specie

Toward a better understanding of direct and indirect trophic interactions between invasive predators and native species on islands

Les prédateurs introduits, tels que les chats (Felis silvestris catus) et les rats (Rattus spp), constituent la principale cause de raréfaction et d'extinction d'oiseaux insulaires. L'impact de la prédation sur les populations d'oiseaux est généralement quantifié grâce à l'identification morphologique des restes d'oiseaux dans les échantillons alimentaires de prédateurs. Une synthèse bibliographique réalisée dans cette thèse soulève les biais qualitatifs et quantitatifs liés à la difficulté d'identification des restes d'oiseaux. Les méthodes moléculaires permettent aujourd'hui de détecter et d'identifier avec précision l'ADN de proies cibles dans le régime alimentaire des prédateurs. Une part importante de cette thèse a consisté à optimiser le protocole moléculaire et en particulier les étapes de sélection des amorces taxon-spécifiques et de l'extraction de l'ADN des proies. La comparaison des performances des méthodes morphologique et moléculaire a mis en évidence la puissance de cette dernière dans la détection et l'identification des espèces d'oiseaux consommées par les chats et rats de l'île de Niau (Polynésie Française). L'étude des interactions trophiques directes (prédation) et indirectes (compétition alimentaire) entre trois prédateurs invasifs (R. exulans, R. rattus et F. s. catus) et un oiseau menacé d'extinction, le Martin-chasseur des Gambier (Todiramphus gambieiri) a montré un très faible impact sur cet oiseau par prédation, mais un fort potentiel de compétition alimentaire avec les 2 Rattus sp., en particulier pour les lézards Scincidae et certains arthropodes terrestres. Des perspectives de conservation du Martin-chasseur sont proposées et discutées.Introduced predators, particularly cats (Felis silvestris catus) and rats (Rattus spp) are recognized as a major factor of rarefaction and extinction of island bird species. The impact of predation on bird populations is usually assessed through the morphological identification of bird remains in predator diet samples. A review conducted in this thesis highlighted the qualitative and quantitative biases related to the difficulty of detecting and identifying the consumed bird species in predator diet samples. Molecular methods allow the accurate detection and identification of targeted prey DNA in the diet of predators. A large part of the work entailed here has been to optimize the molecular protocol and particularly the key steps of the selection of.taxon-specific primer pairs and the extraction of prey DNA. A comparative study of the performances of both morphological and molecular methods highlighted the strength of the latter in the detection and identification of the bird species preyed by cats and rats on Niau island (French Polynesia). The study of the direct (predation) and indirect (competition for food) trophic interactions between three invasive predators (R. exulans, R. rattus and F. s. catus) and a critically endangered bird, the Tuamotu Kingfisher (Todiramphus gambieiri), demonstrated a very low impact of cats and rats on the population of Tuamotu Kingfisher through predation, but a high potential for food competition between this bird and the two species of rats, particularly for lizards (Scincidae) and some terrestrial arthropods. Finally, management perspectives regarding the conservation of Kingfisher Gambier are proposed and discussed

Assessment of invasive rodent impacts on island avifauna: methods, limitations and the way forward

International audienceBird conservation is nowadays a strong driving force for prioritising rodent eradications, but robust quantitative estimates of impacts are needed to ensure cost-effectiveness of management operations. Here, we review the published literature to investigate on what methodological basis rodent effects on island bird communities have been evaluated for the past six decades. We then discuss the advantages and limitations of each category of methods for the detection and quantification of impacts, and end with some recommendations on how to strengthen current approaches and extend our knowledge on the mechanisms of impacts. Impact studies (152 studies considered) emphasised seabirds (67%), black rats (63%) and the Pacific Ocean (57%). Among the most commonly used methods to study rodent impacts on birds were the observation of dead eggs or empty nests while monitoring bird breeding success, and the analyses of rodent diets, which can both lead to misleading conclusions if the data are not supported by direct field evidence of rodent predation. Direct observations of rodent–bird interactions (19% of studies) are still poorly considered despite their potential to reveal cryptic behaviours and shed light on the mechanisms of impacts. Rodent effects on birds were most often measured as a change or difference in bird breeding parameters (74% of studies), while estimates of bird population growth rates (4%) are lacking. Based on the outcomes of this literature review, we highlight the need for collecting unbiased population-level estimates of rodent impacts, which are essential prerequisites for predicting bird population growth scenarios and prioritisingtheir conservation needs. This could be achieved by a more systematic integration of long-term monitoring of bird populations into rodent management operations and modelling bird population dynamics. We also strongly recommend including various complementary methods in impact assessment strategies to unravel complex interactions between rodents and birds and avoid faulty evidence. Finally, more research should be devoted to a better understanding of the cases of non-impacts (i.e. long-term coexistence) and those impacts mediated by mechanisms other than predation and ecosystem level processes

Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances

While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the predator food bolus and have proved themselves efficient, with high accuracy. When studying complex diet samples, the extraction of total DNA is a critical step, as PCR inhibitors may be co-extracted. Another critical step consist in carefully select suitable group-specific primer sets that should only amplify prey DNA from the targeted taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analyzed using both morphological and molecular methods. We tested a panel of 30 PCR specific primer sets targeting Bird, Invertebrate and Plant sequences and four were finally selected to be use as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp DNA stool mini kit, DNeasy mericon food kit and two CTAB-based methods) were compared using four variables: DNA concentration, A260/A280 absorbance ratio, food compartment analyzed (stomach or fecal contents), total number of prey specific PCR amplification per sample. Our results clearly indicate that the A260/A280 absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy mericon food kit (Qiagen), which yielded results very similar to those achieved with the morphological approach

Alignment of group-specific primer set regions

Sequence alignment of DNA regions targeted by the four group-specific primer pairs amplifying Bird, Invertebrate and Plant (mitochondrial and chloroplastic) DNA. Target and non target species were aligned for each group-specific primer pair. Target species were chosen to be as much as possible divergent in order to highlight the potentiality of each primer pair to amplify a wide prey diversity. "N" represents unavailable nucleotide in the existing Genbank sequence, "-" indicates gap and nucleotides between brackets indicate insertions. Note that because Animals do not have chloraplastic DNA, only sequences from target species were aligned for the Plant chloroplastic primer pair

Metabarcoding reveals waterbird diet in a French Ramsar wetland: implications for ecosystem management

International audienceEnvironmental and/or climate changes, occurring at a global or local scale, can significantly impact the diets, health, and population dynamics of waterbirds. This study aimed to develop an effective tool, using DNA metabarcoding of fecal samples, for monitoring waterbird diets during the breeding season in a Ramsar freshwater wetland in Northern France. We collected bird feces across eight marshes with varying anthropic usage. The majority of samples (69%) were from five waterbird species: Eurasian coot ( Fulica atra ), Eurasian moorhen ( Gallinula chloropus ), mallard ( Anas platyrhynchos ), mute swan ( Cygnus olor ), and grey heron ( Ardea cinerea ). DNA was extracted from 116 samples, with plant and invertebrate primers used to undertake multi-marker metabarcoding. Despite a negative impact of uric acid on DNA amplification, we observed significant dietary variations among bird species and sampling sites. Wetland bird diets primarily consisted of four arthropod families, dominated by Chironomidae and Asellidae. The number of plant families detected was higher, consisting of 33 families, with Poaceae highly prevalent within wetland bird diets. This study shows that using DNA metabarcoding to explore interactions between waterbirds and trophic resources is a promising approach to assist wetland management and assess the effect of environmental changes

First steps in studying cat movement behaviour through VHF tracking at a major world breeding site for the Mediterranean endemic Yelkouan shearwater

International audienceno abstrac

First steps in studying cat movement behaviour through VHF tracking at a major world breeding site for the Mediterranean endemic Yelkouan shearwater

International audienceno abstrac

Methods for comparing theoretical models parameterized with field data using biological criteria and Sobol analysis

Prey-predator models are frequently developed to investigate trophic webs and to predict the population dynamics of prey and predators. However, the parameters of these models are often implemented without empirical data and sometimes chosen arbitrarily. Furthermore, when the sensibility of the model to its parameter values is tested, only a few parameters are tested and different prey-predator models (in terms of predation function structure, for example) are rarely compared. Here, we propose a method to compare four prey-predator models for two populations and select the more biologically plausible one to model a simplified agricultural trophic system, including one predator compartment (the red fox Vulpes vulpes) and one prey group compartment (small mammals). These models are based on various Holling functional responses for the predation interaction and take the prey intrinsic growth into account through a Verhulst logistic function. Most parameters values (like attack rates or growth rates) were calculated from field data or based on literature review. Uncertainty quantification is a recent trend that has gained popularity in engineering fields. In this vein, we used Sobol indices to conduct parameter exploration around mean parameter values to investigate and compare the model dynamics responses. Our first results showed that under our assumptions, the two most relevant models for our study case are the saturated Holling I and II models. Furthermore, we were able to discriminate which were the most sensitive parameters in each model. These first encouraging results open the way for the next step, which will be to adapt this model construction to more complex prey-predator systems, with several predator and/or several prey compartments

Rscrit_Consensus_ADOFA_QI_ZL2017

R script to generate consensus genotypes and calculate genotyping error rates (ADO; FA) and Quality Inde